If you have added a Room to a Rate and it's not showing even though you have availability, it could be one of the following reasons:
Do you have pricing on the rates you are looking at for this room
If you don't then the room will not show. Even if you do have pricing, it's best to go back in and Save Changes again on the pricing.
Are there any closed Restrictions in place
Do you have any Restrictions either Rate or Rate x Room restrictions on the dates that the room should be available.
Are there any sell restrictions in place
Have you placed sell Restrictions on the room at the rate level that if a certain amount of that room sell then it is no longer available?
Check Inventory
Just be sure to check inventory again after adding the room to be sure you have inventory.